


The Catalyst

by Jayde_Amali



Category: Mass Effect
Genre: Alternate Universe, Indoctrination Theory, M/M
Language: English
Status: In-Progress
Published: 2012-12-15
Updated: 2013-06-20
Packaged: 2017-11-21 04:17:26
Rating: Mature
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 14
Words: 8,304
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/593360
Author URL: https://archiveofourown.org/users/Jayde_Amali/pseuds/Jayde_Amali
Summary: <blockquote class="userstuff">
              <p>The catalyst isn't quite what people seem to think it is. A/U story. Post ending.</p>
            </blockquote>





	1. The Beginning

No man's land. That's what they called the hell that they were going into. Kaidan Alenko and Joshua Shepard cast a single glance at each other. They knew how likely it was that this was the end for at least one of them, if not both.

"If the two of you are ready, let's go show these bastards what we're made of." James Vega smirked a little as Shepard glared and Kaidan blushed.

Shepard motioned for the two of them to move out, Kaidan on the left and Vega on the right. Shepard took the position he was most efficient with. Right up the center.

Vega would never admit it, but watching the Sentinel and Vanguard literally crush enemies in the way was like watching the Russian ballet troupe perform Swan Lake. Damn, they worked well together. He only had to keep husks from sneaking in behind them.

"Shepard! Watch your ass!" Kaidan flared blue and threw a stasis field around the brute about to charge.

Shepard turned to see the thing and charged at a dizzying speed. He immediately flung a nova, letting the energy fly out around him. He'd seen the four husks nearby. They flew back, though the brute was barely stunned. Shepard's barrier was down and the brute had broken from stasis. It's target was close by and had no shields.

Kaidan was tangling with two husks that seemed determined to bring the Sentinel down. That left James Vega to act as Shepard's backup. The marine let out a shout that caught the brute's attention just long enough for Shepard to scramble behind cover before the bullets went flying.

Shepard leaned out of cover long enough to shoot at the brute. This close and he opted for his shotgun. Once Kaidan was done wrestling with the two husks, he added his personal attention to taking down the brute. With all three, the brute went down quickly. As soon as it fell, another took it's place.

"Well... Shit." James sighed. "How many more of these assholes do we have to go through anyway!"

"As many as it takes, Vega." Shepard didn't seem the least bit nervous or scared, or anything really. Vega might have felt a little better if there was at least some emotion.

"No offense, Loco, but I think you may have long passed the realm of loco." James shakes his head and takes down the latest husk to charge at them.

"Took you this long to realize that, LT?" Kaidan smirked at James. "I could have told you that about him after Rannoch."

Shepard leaned out of cover only to duck back to narrowly miss being hit by a marauder. "Fuck!"The word was ripped from him without a thought.

"Hold that thought for later, Commander." Kaidan chuckled and lifted the marauder for easier targeting.

James rolled his eyes and stood up, firing on the marauder.

Shepard did the same. "Careful, Major. I might not be able to resist your charm."

James groaned. They were going to drive him crazy before the end of this.

Soft emerald eyes stared into pained chocolate ones. A gentle hand pressed against Kaidan's cheek. "I'll always love you, Kaidan."

"Don't leave me behind, please." Kaidan tried to move forward, but James had a strong hold on him.

"Go! Now!" Shepard ran back into the fight to the beam as the Normandy took off.

The last thing Shepard thought was how strange it was that Harbinger didn't attack the Normandy. Then the beam hit him.

"Status report!"

"Our ground team was decimated."

"Why hasn't Harbinger stopped firing?"

"Oh. My. God. It's got Shepard suspended!"

As the reports flew back and forth, no one noticed the waver in the beam. What seemed like an eternity to Shepard, only lasted minutes to everyone else. What everyone did notice was the build up of red surrounding Shepard that unleashed and flew along the beam to hit Harbinger, causing it to release Shepard before crashing to the ground, very much inactive. In the time it took Shepard to fall back to the ground, the Reapers also succumbed to the same fate as Harbinger.

Cheers rose from the soldiers fighting the Reapers and reports started flowing in across the galaxy. Messages were sent to Hackett congratulating him on the success of the crucible, except the crucible had never fired. It had never docked. In fact, it had been destroyed. So how did this happen?


	2. Grief

Kaidan knew he was dreaming. It was always the same. A long hallway that stretched on. Each door he'd open would show him memories of Shepard. Whether it included him or not. This time, the door he opened showed him the day three months ago when Vega stood before him, tears in his eyes, as he held out Shepard's dog tags.

Kaidan shook his head and tried to push the dream away. To change it to something else. Not that day. Just not that day. He ran from the door, stumbling down the hallway. He tried to wake himself up. He tried so hard to just wake up. It wasn't happening. No, something else had to happen first. He knew it was coming.

"Kaidan," came the ghostly whisper. Joshua Shepard's voice. "Kaidan."

"Where are you!" Kaidan screamed.

"Kaidan."

"Damn it, Josh. Tell me where you are!" Kaidan tripped over his own feet and went sprawling to the ground.

"Come to me, Kaidan."

Kaidan began screaming.

"Kaidan. Kaidan!"

Kaidan's eyes flew open and he jerked upright. He nearly headbutted James Vega, who was holding on to his shoulders.

"Jesus! You were screaming like someone was killing you." James let go of Kaidan. "Again."

Kaidan rubbed his eyes and shook his head. "Sorry." He muttered.

"Same dream?" James sat down on the edge of the bed and looked at Kaidan. The man was suffering, no doubt. He looked as if he hadn't slept for days.

"Yeah. It's always the same. I know it's a dream, but I can't stop it." Kaidan flopped back on the bed, flinging his arm over his eyes. "I just can't believe he's dead, James."

James nodded. "Yeah, we all feel that way, man." He shrugged. "I know he cheated death more times than anyone had a right to, but damn, he had to lose sometime."

Kaidan grumbled and glared at James. "You know, you can be a real asshole."

James smirked and shrugged again. "Yeah, I get that a lot." He sighed. "Sorry. Want me to stay?"

Kaidan hesitated before nodding. "Yeah. It helps." He moved over slightly in the bed, rolling on his side, letting James lay down next to him. He felt the warmth of the other man's chest pressing against his back and a strong arm around him. It wasn't Shepard, but it did help. When he went back to sleep, he knew the dream wouldn't return. Not that night, anyway.


	3. Day 1

Kaidan sighed as he read the message from Hackett. Great. Just great. He'd only had a little over three months to recover and now they wanted to send him on some all important mission. He packed a few things, hesitating before deciding to take Shepard's dog tags from their place in his drawer. He found himself wishing that James had stayed in his room last night before sitting down and groaning. No, making himself feel guilty wouldn't help. He rubbed his temples lightly and winced. This wasn't going well at all today. Kaidan grabbed a painkiller and quickly took it hoping that maybe, just maybe, it would keep the migrane at bay. He grabbed his gear and headed out.

When Kaidan arrived for his briefing, he was a little surprised to see James already there. He dropped his bag down next to James' gear. "They got you on this too?"

James nodded. "Yeah. Only they won't tell me what's up. You get anything other than a can't refuse request?"

Kaidan shook his head and winced, rubbing his forehead. "No. Same thing. Came from Hackett himself."

"Migrane?" James frowned as Kaidan barely nodded. "Sorry." He started to rub the back of Kaidan's neck, but was interrupted when Hackett arrived.

"Sorry to keep you waiting." Hackett looked between the two. "I'll be honest. This mission is of the utmost secrecy and does not officially exist." He pauses for the two to acknowledge this. "You'll receive the information en route to Omega."

"Omega?" Kaidan hadn't stopped rubbing his forehead. "Didn't Aria T'Loak take it back?"

"Yes, she did." Hackett nodded. "And that's part of why we're sending you there. The rest is in a sealed file and on your transport. Once you get underway, you'll be able to access the file."

Kaidan nodded. "Understood, sir."

James seemed confused as he shook his head. "If I may ask, why us, sir."

"I believe the file will answer that question." Hackett looked at Kaidan, then James, then back to Kaidan. "As I said, this mission does not officially exist. You aren't here. You never saw that file. You never spoke to me. If you are captured, the Alliance will disavow any knowledge of the two of you being there. Clear?"

"Yes, sir," came from both Kaidan and James. Both saluted and received an answering salute before Hackett left the two of them alone.

"Now what the hell do you suppose is going on?" Kaidan asked James.

"No fucking clue. I guess we should get to our transport and head out. That way we can find out." James picks up his gear and Kaidan's. He smirked a little as Kaidan just sighed and followed along.

Once on board, James took control and piloted the shuttle to the Sol Relay and set their course for Omega. After the shuttle went through the relay, the file that Hackett mentioned unlocked.

Kaidan downloaded it to a datapad and went into the back to read.

James set the autopilot and leaned back for the ride. He had just closed his eyes when he heard a thump thud from the back. He was out of his seat and into the back.

Kaidan was on the floor, leaned up against the wall, datapad held loosely in his hands. He was staring at it, mouth open, and white as a ghost.

"Kaidan?" James sat down next to Kaidan. "What's wrong?"

Kaidan didn't answer. He just sat there unmoving.

James took the datapad and looked at it. He frowned, then read the file again. "What the fuck?"


	4. Omega

When the shuttle docked, Kaidan and James were met by a Turian. They were escorted to Aria in Afterlife. She didn't look at them as she spoke. "What I want to know is what a Spectre is doing out here?"

Kaidan sighed and shook his head. "I'm not here on Spectre authority. I'm looking for someone."

Aria turned around and sat down, crossing her right leg over her left. "He's not here. Left two days ago." She inclined her head toward the sofa perpendicular from her.

Kaidan sat down and leaned forward, elbows on his knees. "Where is he?"

Aria shrugged. "Don't know. Don't care."

Kaidan snorted and looked at James. He stood up. "Come on. We're wasting our time here."

Aria raised a brow. "I didn't say you could go." She smirked as guns were drawn and aimed at the two humans.

Kaidan very slowly turned to face Aria, counting to ten as he did. "Look, if he's not here, then I have no reason to stay. I'm not looking for trouble. So, we'll just go and stay out of your way. In fact, I have every intention of leaving this place. Okay?"

Aria smiled at Kaidan. "And if I say you can't leave?"

Kaidan sighed. "Then I will have to pull Spectre authority."

Aria chuckled darkly. "Shepard tried that once. He learned that I just don't give a fuck about Spectre authority. You're on Omega. You follow my rule."

Kaidan smiled slightly. "Yeah, he mentioned that rule. Don't fuck with Aria."

Aria laughed and nodded. "That's the one."

Kaidan stopped smiling. "And I have no intention of breaking that rule."

Aria was silent for a long moment, just looking at Kaidan. "Fine. Go." As Kaidan turned to leave. "Oh, there is one more thing."

Kaidan looked back at Aria. "What?"

"The person you're looking for?' Aria smirked. "He said if you came here to give you this." She tossed a datapad at Kaidan.

Kaidan caught it and nodded. "Thanks."

"Now get out of here. Humans aren't exactly welcome around here right now." Aria nodded to her guards.

"Thanks for the warning." Kaidan motioned to James and the two left for their shuttle. They didn't complain about the Turian following behind them.

Once back aboard the shuttle, James and Kaidan sat down to discuss their strategy before leaving.

"So, we going back to Earth, no?" James started up the shuttle's engine and waited for clearance to leave.

Kaidan, however, didn't respond. He was too busy reading from the datapad. He had gone white again.

James looked over at Kaidan. "Hey, we going back..." He trailed off. "Kaidan? What is it?" No response. "Hey, Kaidan?" He reached over and snapped his fingers in front of Kaidan's face. "Major!"

Kaidan blinked at the snapping. "No. We're going to Horizon." His voice was hollow.


	5. Day 2

Upon nearing Horizon, James let out a string of curses.

"What's wrong?" Kaidan leaned over to see.

"We got Reapers! That's what's fucking wrong!" James started to turn the shuttle around.

"Wait, James. I have to go down there. I have to know." Kaidan somehow remained calm.

James just stared at Kaidan for a moment, then nodded. "All right, but I'm going with you. And we're both going fully armed."

Kaidan nodded and leaned back. "How many Reapers?"

"One big one. I think Sovereign class." James shrugged. "It's not one of the little ones that Shepard nailed on Tuchanka or Rannoch, that's for sure." He passes the data over for Kaidan to see.

Kaidan barely glanced at it. "Yeah, it's as big as Sovereign was." He shrugged. "So one big one and lots of little ones."

James nodded. "Yeah, that's about it." He turned to look at Kaidan for a long moment. "You really think he's down there?"

Kaidan shrugged. "I don't know." He looked at James with haunted eyes. "But like I said, I have to know."


	6. The File

This unofficial mission is to confirm the reports of rumors regarding possible Reaper survivors in the Terminus systems. Reports have come in that these survivors may have been instrumental in assisting Aria T'Loak taking back Omega. You are to determine if this occurred but you may not approach Aria directly. If she's working with the Reapers, we don't want to tip her off that we know. If you are unable to find out, report back to Earth immediately.

One other thing. There have been some rumors that Commander Joshua Shepard may not be dead, but indoctrinated and working with these Reaper survivors. If he is spotted, you are under direct orders to apprehend him and return him to Earth. If you cannot apprehend him, then he must be killed.

I know I'm asking a lot of you, Kaidan. I do know about the relationship you've shared with Shepard. I cannot, in good conscience, ask anyone else to do this because you know him best. I'm sending Lieutenant Vega with you for support. I'm aware he's your roommate and has helped you through a difficult time. If you cannot take the shot, I'm asking for Lieutenant Vega to do so.

S. Hackett


	7. Horizon

The shuttle touched down at the site of the old colony where Kaidan had been assigned. Both he and James were suited up and armed. So far, there were no signs of reapers nearby. The place seemed deserted.

Kaidan slid open the hatch and James jumped out, rifle ready. When Kaidan heard the all clear, he joined James on the ground.

James finally lowered his rifle. "So this is where you were stationed?"

Kaidan nodded. "Yeah. The Collectors took half the colony and Shepard came in to save our asses. I was one of the lucky ones."

James looked at Kaidan for a moment, then nodded. "Yeah, I guess you were. So, are you gonna tell me what was on that datapad?"

Before Kaidan can answer, a very familiar voice speaks from behind them. "I thought I told you to go home, Kaidan." That voice is laden with half anger and half amusement.

Both Kaidan and James turn, though James is the only one to aim his gun. Kaidan doesn't hesitate. His biotics kick in and he unleashes a throw that sends Shepard half way across the landing zone.

"Dios, Kaidan. We're not supposed to kill him first." James lowered his rifle.

Kaidan just stared at James for a moment, eyes blank. "If I wanted to kill him, I'd have sent him into something. Not just skidding across the ground."

Shepard stands up, dusting himself off. "Yeah, okay, I deserved that."

"You deserve a bullet in your back!" James spat out, rifle aimed again.

Kaidan raised a brow at the harsh tone before looking back at Shepard. "Why? Why did you let everyone think you were dead? Why did you let me go through that hell again?" He's screaming by the end, not caring.

Shepard frowned at Kaidan, then shook his head. "I didn't... I told Hackett everything... What?" He rubbed at his forehead. "Kaidan..."

Kaidan shook his head and crossed over to Shepard, standing inches away from him. "Hackett sent us out here on rumors. Rumors that you were alive and working for the fucking reapers! We're either to arrest you or kill you, damn it!"

Shepard couldn't speak. For once, he was stunned into silence.

James moved closer, keeping his aim on Shepard the whole time. "Well? You gonna answer?"

Shepard closed his eyes and rubbed his temples. "It's a little overwhelming when you find out that someone you thought was an ally sends the two people that you care about most to kill you."

James frowned, then finally lowered the rifle. "I take it that means you won't cooperate, no?"

Shepard's pained eyes turned to James. "I can't. Hackett knew that already. He knew I wouldn't leave."

Kaidan tried to speak, but a sound somewhere between a choke and a sob starts to form before he cuts it off. He turned away, closing his eyes.

James barely nodded, his eyes starting to sting. He lifted the rifle and fired.


	8. The Message

If you're reading this, then you've been to Omega. Turn around. Go home. The Terminus Systems are not safe right now. Let me repeat that. Go. Home. Kaidan.

If you're still reading this, then you're as stubborn as I am. God, Kaidan, please, just listen to me and trust me. You can't be out here right now. I can't go into it in this. Not with Aria giving it to you. Hell, even she's probably told you to get the fuck out.

Okay, so, I know you're still reading this now and have no intention of going home. Hackett probably sent you because of rumors. Stupid rumors. If you have to find me, go where you met me the first time for the second time. I'd rather you didn't, but I know you, Kaidan. Just be careful. Don't come out guns blazing. Please. Trust me.


	9. The Normandy

The shuttle docked with the Normandy two days later. Both Kaidan and James were met by Hackett in the shuttle bay.

Kaidan couldn't look Hackett in the eyes. He kept his gaze down at the floor.

James, however, saluted, then commented, eyes accusatory and harsh tone. "Officially, sir, the mission was a success."

Hackett nodded and rubbed his chin. "Unofficially?"

Kaidan looked past Hackett. That was when the hatch slid shut and Hackett was thrown up against the wall.

The first thing Hackett realised was the shotgun pressed up against his chin. The second was the angry green eyes only inches from his own.

"Shep-" Hackett started, then grunted as the shotgun was pushed further into his chin.

"What the fuck is going on?" Shepard growled. "You sent them out here to kill me, you son of a bitch."

Hackett tried to swallow past the gun. "Stand down, Commander."

"Fuck you." Shepard spit out. "I'd pull the trigger right now if I thought for one second it'd solve the problem."

"It wasn't my call, Joshua." Hackett said calmly.

"Then who's was it?" Shepard let the shotgun retreat a little.

"Admiral Johnson. She got the others on her side. Now, if you're going to pull the trigger, do so. Otherwise, stand down, Commander." Hackett leveled his gaze on Shepard, devoid of emotion.

Shepard was silent a moment, his eyes searching Hackett's for something, then released him. He attached his shotgun to the back of his armor. "Sorry, sir. I had to determine if you were a threat." He didn't sound too apologetic.

Hackett raised a brow. "You'd better have a damned good reason for your actions, son."

Shepard sighed. "Someone in Alliance Command is indoctrinated. We don't know who." He sat down and looked up at Hackett. "I didn't think it was you. Honest. I just had to be sure."

Hackett sat down next to Shepard. "You could have just sent me a message."

Shepard shook his head. "No. Not with this information." He looked at Hackett. "Why didn't you tell Kaidan like I'd asked?"

Hackett leaned back and looked between Shepard and Kaidan before settling his gaze on Shepard, not able to meet the glare Kaidan had fixed on him. "Wasn't my choice. Johnson got word that I'd received an encrypted message from you. I was going to let Major Alenko know, but she strongly suggested we investigate first. I had to agree. We didn't know if it was really you sending the message. Eventually, she convinced the others that you were indoctrinated and had to be killed. They wouldn't listen to me." He finally looks at Kaidan. "I let you know the only way I could. That file you read was likely to be hacked. This had to look real."

Shepard closed his eyes and rubbed his temples. "I get it. You sent Kaidan and James because you knew they wouldn't be able to make the killing shot." He rubbed his left shoulder. The blood on his armor was still fresh. He looked at James. "And I'm damned glad you're a good shot."

James smirked and half saluted Shepard.

Hackett nodded. "Exactly. They both served with you. You and Major Alenko may have been discreet, but it got back to us. We knew about your relationship. Lieutenant Vega has been at your side through all this as well. He respects you a great deal. I didn't think he'd have been able to take the shot. I'm glad I was right."

Shepard couldn't do more than shake his head. "Okay. Okay. I can't go back to Earth right now, but I need to be in the same room as Johnson. If she's indoctrinated, her reaction to me will show it."

Hackett considered that for a moment, then nodded. "I can always request for those involved in this decision to come to the Normandy to debrief the infiltration team themselves. We can spring them on you then." He rested a hand on Shepard's shoulder briefly, then stood up. "Until then, I need to restrict your movements. The old XO's office is available. We'll stash you there."

Shepard just laughed without humor. "So, I'm actually under arrest then?"

Hackett shook his head. "Oh, no. I just don't want word getting out that you're on board. Johnson needs to believe you're dead." He looked at James. "Clear a path, Lieutenant. I don't want anyone seeing Shepard." He turned to Kaidan. "And you're going to be guarding him, Major. No one is to see him except for the Lieutenant, you, and myself. Understood?"

Kaidan nodded with a small smile forming. He looked at Shepard, then held out a hand. "Looks like we'll have a bit of free time."

Shepard took the offered hand and stood up. "Looks like it." He nodded to Hackett. "Thank you, sir."

Hackett shook his head. "Don't thank me yet, Commander. We still have a job to do."

Shepard nodded. "Yes, sir."


	10. A Little Downtime

Shepard sat on the bed, back against the wall, legs stretched out in front of him. His eyes were closed as he listened to Kaidan talking to him.

Kaidan sat in a chair near to the bed, feet up on the bed. He looked up from the datapad, then sets it down in his lap. "And, Joshua Shepard, are you even listening to me?"

Shepard doesn't open his eyes, but he nodded. "Mmm-hmm."

Kaidan crossed his arms over his chest. "So? What did I just tell you?"

Shepard opened his eyes then shrugged. "I dunno. You asked if I was listening to you, not listening to what you were saying."

Kaidan tried not to smile. Oh, he tried. He failed. He shook his head. "Jerk." He had to laugh. He swung his legs down, then sat on the bed next to Shepard. "Well, if you'll be so kind as to listen to what I have to say, you'll learn something."

Shepard nodded. "Okay. What?"

Kaidan took hold of Shepard's hand. "Just stay calm, okay?" He waited for Shepard to nod. "Hackett gave me the list of those who will be there for the debriefing. Your mother's on it."

Shepard drew a sharp breath, then let it out slowly. "I hope she's not indoctrinated."

Kaidan nodded, then moved slightly so his arm was around Shepard's shoulders.

Shepard leaned in against Kaidan. "You need to know, Kaidan, that I'm going to kill whoever's indoctrinated."

Kaidan tensed a little, but nodded. "Should I warn Hackett?"

Shepard nodded. "Probably should. If he gets in the way, I'll go through him. I don't want to have to do that." He twined his fingers together with Kaidan's.

It was Kaidan's turn to draw a sharp breath. "What the fuck? Shepard?"

Shepard looked at Kaidan for a moment, then sighed. "Kaidan, I respect Hackett a great deal. I don't want to have to kill him, but I will if it means killing whoever is indoctrinated."

Kaidan shook his head. "And if it's your mother?"

Shepard was silent for a very long time before sighing. "I'll never forgive myself, but I'll still pull the trigger."

Kaidan tightened his hold on Shepard. "I don't get it, I mean, I know what you told me on Horizon about the whole thing, but this is just insane."

Shepard closes his eyes and rested his head on Kaidan's shoulder. "Yeah, I'm not sure I'd believe it either.


	11. What Happened on Horizon

Shepard blinked several times, cradling his left arm, blood flowing from his shoulder, before being able to respond. "You... actually shot me?" He frowned at James.

James shook his head. "You could have at least had your damned shields up, Loco." He sighed and slung his rifle to his back before approaching and applying medi-gel to Shepard's shoulder.

Kaidan turned back around. "Let the record show that Lieutenant Vega took the shot. Commander Shepard is dead."

Shepard raised a brow. "Except I'm not."

Kaidan rolled his eyes and lifted a hand, caressing Shepard's cheek. "Yeah, you are. Or at least Hackett will think you are." He couldn't smile. He couldn't feel anything.

Shepard covered Kaidan's hand with his own. "Kaidan, believe me, I didn't mean for this to happen."

Kaidan stayed quiet for a moment, just staring at Shepard. When he finally spoke, his voice almost broke. "Just tell me why you did this?"

Shepard closed his eyes for a moment, then opened them to look at Kaidan. "I had no choice. When I was connected to Harbinger, there was so much information dumped in my head that I couldn't make sense of it all. I'm still sorting through it."

James crossed his arms and frowned. "Well, try to explain. I didn't take care of Kaidan for three months for nothing, you know. I was there when you weren't."

Shepard turned his gaze to James. "I know, and thank you for that." He looked back to Kaidan. "When I fell, I was knocked unconscious. I know there were moments where I was in and out. A banshee was carrying me. I remember trying to get free, but she was too strong and I was badly hurt. I just hoped I'd die before they could do anything to me."

Both Kaidan and James flinched at the mention of the banshee. Kaidan removed his hand from Shepard's cheek, though kept hold of his hand.

"The first clear memory I have after all of this was of Vanguard." Shepard jerks his thumb over his shoulder. "The big one out there. He was... singing. I know, it's weird."

James couldn't help it. He actually laughed, breaking the tension. "A singing Reaper?"

Shepard shrugged with a small smile. "Like I said, it's weird. He's not that bad either. He helped me sort through a lot of the information I had gotten from Harbinger. Turns out that not all Reapers are harvesting maniacs. There are some like Vanguard that want to learn about us. Organic life."

Kaidan shook his head. "I don't get it."

Shepard sighed and squeezed Kaidan's hand. "I'm getting to that part. Two hundred million years ago, Vanguard and about a hundred others split off from the main group. They were outcasts. They didn't want any part of the harvest anymore."

"If that's true, then why are they out here hiding?" Kaidan interrupted again.

"Because not all of Harbinger's group was killed when I was unleashed and would you trust a Reaper?" Shepard glared at Kaidan. "Now shut up and let me talk." He waits for Kaidan to nod before continuing. "The Crucible was a lie. The Catalyst being the Citadel was a lie. Harbinger was responsible for the plans for the Crucible getting started. He was also responsible for the rumor about the Catalyst being the Citadel. He rather enjoyed watching organics scurry around trying to finish what they thought was their only hope."

James started to say something, but stopped when Shepard looked at him. He shrugged apologetically, then leaned up against a crate, motioning for Shepard to keep talking.

"Vanguard's group was waiting for the Catalyst. The Reapers knew that eventually genetics would produce someone immune to them. Someone that had enough power to subvert theirs and allow them to be killed a hell of a lot easier than it should have been. When Sovereign was destroyed, Harbinger, well, fucking freaked out. He had learned of me through Sovereign and became fascinated with me."

Kaidan shook his head. "Who wouldn't?"

Shepard smirked at Kaidan, then continued. "Vanguard and his followers found out what Harbinger was up to and sent their own troops in. They managed to subvert and control quite a few ground troops to help. They were always there, believe it or not. They kept an eye on me the entire time, making sure I survived. During the final push for the beam, Harbinger captured me. Some kind of connection forged between us that allowed me to see everything he knew. He became fucking terrified of me during that, and that's putting it lightly. I didn't know why at first, but then I saw it. I knew what I was."

"The catalyst," came James' soft whisper. "You're the fucking catalyst."

Shepard nodded at James. "Yeah. I wanted Harbinger and the Reapers dead. I didn't know how to do it though, but once I thought about it, it just happened." He shrugged helplessly. "I'm still not sure how it happened."

Kaidan frowned. "So why aren't these ones dead?"

Shepard shrugged. "I think it's because they weren't connected to Harbinger. Some of Harbinger's reapers disappeared from what I could hear while connected to him, so those ones, I'm assuming are the ones that survived. They're out here. It's why the Terminus systems aren't safe."

James looked off toward the Reaper. "So, how, exactly, does Hackett play into all of this?"

Shepard shrugged again. "I wish I knew. I already told him about all of this. All I can guess is that either he's indoctrinated, or someone with some influence over him is. I'd hope it's the latter. In fact, I'm pretty sure it is. I don't think he'd sit on this for two months before taking action if he got his marching orders from the bad guys."

James looked back at Shepard. "So, what do we do about it?"

Shepard was silent, looking off toward the Reaper. He finally looked back to James, green eyes cold. "We find out. Call Hackett. Get him out here. I don't care how. Just do it."

James nodded and headed for the shuttle.


	12. The Debriefing

Minutes before those involved arrived, Kaidan pulled Hackett aside. "Shepard told me to warn you. If any of them are indoctrinated, he's going to kill them."

Hackett shook his head as if physically slapped. "If he's right, then whoever it is will probably try and kill him first. At least I hope that's true. I don't want to have to have him up on charges of murder. He's already facing desertion and treason." He looked toward the door where Shepard was waiting. "I'm giving them a good fight though. If this works out, then maybe, just maybe, those charges can be dropped." He looked back at Kaidan. "Just tell him not to fire the first shot. Quickly."

Kaidan nodded. "Yes, sir." He hurried to the XO's room and stepped inside. "Josh..."

Shepard was just finishing with his armor. "Kaidan?" He seems a little amused, then turns to see the seriousness of the look he's being given. "What did Hackett have to say?"

Kaidan sighed. "Did you know you were up on charges of treason and desertion?" At Shepard's stunned look, he nodded. "Yeah. Hackett is running interference for you. He's trying to get them dropped." He rubbed the back of his neck. "Oh, and he told me to tell you not to take the first shot. If you do, you could be charged with murder as well."

Shepard nodded and snapped the final latch in place. He crossed the room to stand in front of Kaidan. "I'm not stupid, Kaidan. Insane, maybe, but not stupid." He smiled slightly, just letting the corners of his mouth twitch upward.

Kaidan pulled Shepard into a hug. "Just be careful and be right."

Shepard returned the hug before pulling back a bit to look at Kaidan in the eyes. "I will." He leaned in and kissed Kaidan softly before letting him go. "You should get out there. I'll be listening and I'll know when to jump in."

Kaidan nodded and leaned in to kiss Shepard on the cheek. "Let's just hope I can pull off my part."

Shepard chuckled. "Yeah, you're a horrible liar."

Kaidan rolled his eyes and left the room. The deck had been cleared of crewmen and the committee had arrived, each of the nine individuals finding a seat.

James was leaning up against the wall, looking a little more than tense. He nodded as Kaidan joined him. They stood there, just waiting, in complete silence.

Hackett was clear to point out which one Johnson was without alerting her. He caught both James and Kaidan's slight nods.

Kaidan's eyes found Hannah Shepard's and he quickly looked away. When he looked back, he was surprised by the small sad smile she offered him. He returned it, then looked away again.

James muttered softly to Kaidan. "Who was that?"

"Shepard's mother," came the reply. Kaidan saw James' nod.

When Hackett called the meeting to order to debrief Kaidan and James, the noise level died down. Luckily for Kaidan, Hackett asked for James first.

James pushed himself away from the wall and recounted the time on Omega, leaving out the message Kaidan got, instead stating that Horizon was overheard as a possible point of interest. When he talked about Horizon, he stated that he took the shot. He didn't state, however, that it was a killing shot.

Johnson leaned forward. "So, Commander Shepard is indeed dead?"

Before James could respond, the door to the XO's cabin opened and Shepard stepped out. "Not as dead as you'd like to think."

Chaos. That's the only way to describe it. Hannah stands, clasping her hands to her mouth. You think she'd be used to her son escaping death with how often he's managed to do it. The others, with the exception of James, Kaidan, and Hackett, burst into talk, trying to make themselves heard.

A shot rings out over the noise. When the noise dies down, it's not Johnson that's holding a gun. It's her aide. Shepard has his pistol trained on the young marine.

"Drop it, soldier." Shepard's eyes narrow dangerously.

"You shouldn't be alive. You need to die." The aide spits out.

"What is the meaning of this?" Johnson demands.

Shepard doesn't look at her, keeping his eyes on his target. "Your aide is indoctrinated. Now, tell me, why do I need to die?"

The aide's hands begin to tremble a bit. "Because you're not natural. You never should have been born. The Reapers can't do what they need to do with you alive." The aide fires his gun.

Shepard's shields take the hit and another shot rings out. The aide falls back, quite dead when he hits the ground.

Hannah Shepard lowered her own pistol. "Never, ever, threaten my son again." Her words were hissed through clenched teeth.

Shepard rolled his eyes and lowered his gun. He couldn't help the flush that hit him. He lowered and shook his head, rubbing the bridge of his nose.

Johnson looked to be in shock, finally training her eyes on Commander Shepard. "Mind telling me exactly how you knew he was indoctrinated?"

Shepard shrugged. "It was easy. He shot at me."

Johnson looked at James. "And you said you shot him. Were you lying?"

Shepard cut in before James could answer. "Oh, no, he shot me. He just didn't kill me."

James nodded to confirm that. "Sorry, ma'am, but I never did say I killed him."

Johnson leaned back, looking at Shepard for a long moment before nodding. She looked at Kaidan. "In your personal opinion, Major, is the Commander indoctrinated?"

Kaidan shook his head. "No, ma'am, he's not." He looked at Shepard, then let the ghost of a smile touch his lips.

Johnson nodded, but continued. "How can you be so sure?"

Kaidan gave Shepard a questioning look. At Shepard's nod, Kaidan handed Johnson a datapad. "Because of this. He tried to get me to leave the Terminus systems. Had he been indoctrinated, he'd have wanted me to join him instead. He'd never have been able to try and keep me away."

Johnson read the datapad, then looked at Shepard. "Why didn't you return to Alliance space after you had recovered?"

Shepard put his hands behind his back and stood a little straighter. "I decided that it was best to stay where I could do the most good in the fight against what remained of Harbinger's Reapers, ma'am. Had I returned to Earth, they would have followed me there. By staying with Vanguard and the outcasts, I was able, and will still be able, to learn about who I am."

Johnson doesn't look at all convinced. "Commander Shepard, I would be well within my authority to have you arrested now and returned to Earth to stand trial.."

Shepard strides forward, putting his hands on the table in front of Johnson. "For treason and desertion. Yeah, I know, I heard. You do that and you've just signed the death warrant of every living organic being in this galaxy. You wanna know why?" He doesn't wait for a response. "Because there's more of Harbinger's Reapers out there than there are of mine. They'll tear through us without the Catalyst on our side."

The last two sentences hung in the air before Kaidan moved over to Shepard, placing a hand on his shoulder. "Shepard." His voice was soft and uncertain.

"No." Shepard pulled away from Kaidan. "I am Vanguard. Shepard allowed me to respond for all of us when he was threatened with arrest." He looked back at Johnson. "And believe me when I tell you that we will never allow you to take him against his will."

Johnson blinked several times before she could even begin to form a response. By the time she had one, Shepard's eyes rolled back and he hit the floor.


	13. The Aftermath

**Notes for the Chapter:**

> I haven't forgotten about this story, nor will I let it die out. I lost a lot of work I'd had done on it and have been rewriting it since.

The only way to describe what happened next was chaos. When Shepard hit the floor, and after he was taken into the medlab, Johnson was adamant that what they had witnessed was indoctrination.

"There is no way in hell he's indoctrinated, sir." Kaidan shook his head. "It's just not possible. He's the reason we're all still here."

"Don't mean to rain on anyone's parade, but we got a situation up here that I think warrants your direct attention, Admirals." Joker's voice drifted through the comm system, sounding a bit concerned.

"What is it, Joker?" Hackett sounded tired, but still alert.

"We got a big ass reaper headed our way. It's broadcasting on all channels."

"Patch it through down here."

The voice of the reaper bursts through the room. "We are Vanguard. You will return the catalyst. You will return Shepard. You have one hour to comply."

"Or what?" Johnson demanded.

"Or we will board the Normandy and take Shepard by force." The system bursts into static and is cut off.

During the communication, no one noticed Shepard rejoining the group. "Vanguard means it. He will take the Normandy. Just let me go." He started toward the elevator only to be stopped by Johnson.

"Commander Shepard, I have no choice but to place you under arrest for treason and desertion. You will also be tried on suspicion of indoctrination." Johnson motioned for two marines to apprehend Shepard.

Shepard gave no resistance, much to everyone's surprise. He just sighed and shook his head sadly. "By doing this, you're signing the death warrants of the entire galaxy. Vanguard will first take me by force, then he will likely destroy the Normandy, no matter how much I beg him not to. Oh, he might spare a few people here, just because he knows how much they mean to me, but everyone else? Dead. The tenuous influence I have over him will be snapped in two. He'll tap into my darker side. Remember Torfan, Admiral? Remember the Batarians? If Vanguard goes insane, things will be a thousand, no, a million times worse. As it is now, I can keep the peace. He wants what remains of Harbinger's reapers gone. Destroyed. Then he wants to learn about us. Find a way to co-exist peacefully. You're destroying that chance."

Johnson seemed to ignore Shepard's speech and ordered the marines to keep him under house arrest until they returned to Earth. Shepard was taken back to the XO's cabin and left alone, but not before he noticed the slight hand signals from Kaidan and James.

Shepard sat on the floor, closing his eyes. _Vanguard, I know you can hear me. Give me time and I will rejoin you. Johnson doesn't understand. Kaidan and James are going to free me, but it may take longer than an hour. If they stall for time, allow it._

_I hear and will do as you ask, but not for long. I will not allow them to keep you captive._ Vanguard's soft reply came as a mental caress. _You are everything, Shepard._

Shepard smiled faintly, then looked up as the door opened. Johnson stood there, her sharp eyes finding Shepard in the dark room. "It seems you were wrong. Your Reaper isn't taking any action. In fact, it has agreed to provide us with more time."

Shepard can only smile in response, his eyes flaring angrily. "Do you honestly think that by detaining me you will win anything here?"

"We have you, Shepard. We have you. It wants you alive. It won't get you alive. I'll order the self destruction of the Normandy before I hand you over to the enemy."

"Vanguard is not your enemy. In fact, he's one of the few allies we have that is capable of mounting a defense against Harbinger's reapers. Fortunately, he knows that you're not going to destroy the Normandy with me on board. Not when I'm your only bargaining chip. You need me to appease a lot of races." Shepard shook his head. "No, if you're going to kill me, it's going to be in public. You'll want as many people to witness it as possible. Vanguard also knows that, so he's willing to bide his time and wait." Shepard smirked at Johnson's look of surprise. He actually laughed when she turned and stalked out of the room.


	14. The Escape

That evening, just as Shepard was about to fall asleep, he heard two thumps from the other side of the door. He slipped into a spot hidden by shadows and prepared himself for an attack. When the door slid open, relief flooded through him. Kaidan and James stood there in full armor and weapons ready.

"Josh, come on," hissed Kaidan. The look of relief was visible when he saw Shepard slip out from the shadows.

James stood on the other side of the door. "I don't want to break up a teary reunion, but we don't got a lot of time here. Come on." He ignored the double glares of irritation shot in his direction.

The three of them moved through the deck, then down to the cargo bay. Cortez was waiting by the shuttle. When he saw the three of them, he got into the shuttle for a quick pre-flight check.

Shepard was nudged into the shuttle first and came face to face with Hackett. He blinked several times, then was pushed past the Admiral.

Kaidan glanced at Hackett briefly before sliding the door closed behind James.

Hackett nodded, then called out to the front. "Cortez, go." He sat down as the doors were opened and the shuttle left the Normandy.

Shepard frowned at Hackett. "Isn't this some kind of treason?" He shook his head. "Not that I'm complaining about the rescue."

Hackett allowed a faint smile. "Son, you're our only chance of beating the sons of bitches still out there. You and those reapers that seem to think you're their god or something."

Shepard sat down next to Hackett. "I'd say thanks, but this isn't official, is it?"

Hackett shook his head. "No, it's not. There is one thing I'm curious about. I couldn't ask on the Normandy, so I decided to come along." Shepard's brow raised in question. "How is it that Vanguard was able to speak through you?"

Shepard sighed and rubbed his temples to stave off the potential headache that was starting to build. "After Harbinger was destroyed, I was badly hurt. I damn near died. When I was brought to Vanguard, my mind was in shreds. There was too much information that I had gotten from Harbinger. While they could fix my body, the only way to save my mind was for Vanguard to merge with me. It's what Harbinger tried to do. I resisted him, but with Vanguard, it was different. He explained everything that was going on. At first I said no, but I realized that I was getting worse. I couldn't tell the difference between what had happened hundreds of thousands of years ago and what was happening now. I finally agreed to merge with Vanguard in a moment of weakness. I didn't want to die. I expected it to be painful, frightening, and horrifying. Instead, it was pleasant, comforting, and, I know this is going to sound odd, but it was also loving."

Hackett raised one brow, surprised at the description. "So this reaper has emotions?"

Shepard nodded. "They all do. Vanguard's reapers have cultivated different emotions than the rest. It was one of the reasons they broke away."

Kaidan frowned at Shepard. "So you're not you anymore?"

Shepard looked up at Kaidan. "I'm still me. I just have a really freaky bond with a reaper. It could be seen as a form of indoctrination, but both of us are just as affected by the other. He feels what I feel. I feel what he feels. He's angry that I was arrested, but he's in pain because I'm not there."

"You're never coming back, are you?" Kaidan stared at Shepard in disbelief.

Shepard looks back at Kaidan, his eyes conveying his anguish. "I can't, Kaidan. I can't. Vanguard and I are each one half of a whole. We can't be separated. It would kill both of us."

Kaidan turned and went to the front to sit with Cortez. He said nothing further.

Shepard reached a hand out to try and stop Kaidan, but pulled back. "Vanguard wants Kaidan to stay with us. He's really worried about my mental state if I continue to worry about him."

Hackett shook his head. "I'm not ordering him to go. I'm also not ordering him to come back. This entire mission doesn't exist."

James smirked and nodded. "In fact, everyone over there will think we kidnapped the Admiral and Esteban and made them take you back. Kaidan and I already talked about it. We're not coming back. We can do more if we stick around with you."

Shepard looked toward the front of the shuttle, then nodded to James. "Thanks. I owe you one." He started to smile, but the shuttle was lurched sideways. Shepard's head collided with something hard and the last thing he heard was Hackett screaming for the Normandy to cease firing.


End file.
